For anyone that runs into this, I found the issue.
Several of my custom templates must have had a small sized (1/4 screen or so) Multidock height set, so this setting was "sticky" and was always opening in a small size. This was really annoying when doing Melodyne regions 20-30 times in a session, as you're always resizing. I just never saw a way to "reset" this sticky setting. Now I do.
The trick: close your Multidock.
Next, mouse grab the boundry for the "closed multidock" and manually open it to the size that fits your workflow.
Hit "D" to close it.
Next time it opens, the larger size will be "sticky" as it should be and everything you open in the Multidock will open to that size.
Oh, and yes the Screensets would be a good workaround, but I knew this behavior was not correct so I'm glad to have found the cause and fix. Thanks for helping work through it :)